Locus 5119

Sequence ID	X_DroMel_CAF1
Location	13,368,189 – 13,368,285
Length	96
Max. P	0.836949

overview

Window 1

Location	13,368,189 – 13,368,285
Length	96
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	77.25
Mean single sequence MFE	-28.09
Consensus MFE	-12.31
Energy contribution	-13.03
Covariance contribution	0.72
Combinations/Pair	1.14
Mean z-score	-2.06
Structure conservation index	0.44
SVM decision value	0.67
SVM RNA-class probability	0.817086
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13368189 96 + 22224390
-U-UGGGCAAAAGAGGGGUUUAUUAUACUUCAGAACCAGCCUGUUG--UCGGCCUUUCU--UCAUUU-----GCCA----------CUUUCUUGUUCCUGCUU---UUCGCAUGGACAUU
-.-..((((((.(((((((((...........))))).(((.....--..)))....))--)).)))-----))).----------......(((((.(((..---...))).))))).. ( -27.20)
>DroSec_CAF1 14221 97 + 1
UU-UGGGCAAAAGAGGGGUUUAUUAUACUUCAGAACCAGCCUGUUG--UAGGCCUUUCU--UCAUUU-----GCCA----------CUUUCUUGUUCCUGCUU---UUCGCAUGGACAUU
..-..((((((((((((((((((.......(((.......)))..)--)))))))))))--...)))-----))).----------......(((((.(((..---...))).))))).. ( -28.60)
>DroSim_CAF1 13962 97 + 1
UU-UGGGCAAAAGAGGGGUUUAUUAUACUUCAGAACCAGCCUGUUG--UCGGCCUUUCU--UCAUUU-----GCCA----------CUUUCUUGUUCCUGCUU---UUCGCAUGGACAUU
..-..((((((.(((((((((...........))))).(((.....--..)))....))--)).)))-----))).----------......(((((.(((..---...))).))))).. ( -27.20)
>DroYak_CAF1 15305 105 + 1
UUUUGGCCAACAGAGGGGUUUAUUAUACUUCAGAACCAGCCUGUUGUGUUGGCCUUUCU--UCAUUUGUCUUGCCA----------CUUUCUUGUUCCUGCUU---UUCGCACGGACAUU
....((((((((((.(((((.................))))).)).)))))))).....--...............----------......(((((.(((..---...))).))))).. ( -26.13)
>DroAna_CAF1 14722 113 + 1
UG-CGAGGGAAAGAGAAGUUUAUGAAACUUCAGUGCCAGCCUGUUGCCCCGUCCUUUCUCAUCAUCU-----GGCGGCCUGCCCCGCCUC-CUCCCCCCGCCCAGCUCUGGCCGGACAUU
..-.(((((((((.((((((.....)))))).......((.....))......))))).........-----(((((......))))).)-)))...(((.(((....))).)))..... ( -31.30)
>consensus
UU_UGGGCAAAAGAGGGGUUUAUUAUACUUCAGAACCAGCCUGUUG__UCGGCCUUUCU__UCAUUU_____GCCA__________CUUUCUUGUUCCUGCUU___UUCGCAUGGACAUU
....((.....(((((((((..........(((.......))).......)))))))))..)).............................(((((.(((........))).))))).. (-12.31 = -13.03 +   0.72)

alignment

secondary structure

dotplot

Window 2

Location	13,368,189 – 13,368,285
Length	96
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	77.25
Mean single sequence MFE	-28.50
Consensus MFE	-9.32
Energy contribution	-10.16
Covariance contribution	0.84
Combinations/Pair	1.07
Mean z-score	-2.07
Structure conservation index	0.33
SVM decision value	0.74
SVM RNA-class probability	0.836949
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13368189 96 - 22224390
AAUGUCCAUGCGAA---AAGCAGGAACAAGAAAG----------UGGC-----AAAUGA--AGAAAGGCCGA--CAACAGGCUGGUUCUGAAGUAUAAUAAACCCCUCUUUUGCCCA-A-
..(((((.(((...---..))))).))).....(----------.(((-----(((.((--((((.((((..--.....))))..))))...((.......))...)).))))))).-.- ( -23.20)
>DroSec_CAF1 14221 97 - 1
AAUGUCCAUGCGAA---AAGCAGGAACAAGAAAG----------UGGC-----AAAUGA--AGAAAGGCCUA--CAACAGGCUGGUUCUGAAGUAUAAUAAACCCCUCUUUUGCCCA-AA
..(((((.(((...---..))))).))).....(----------.(((-----(((.((--((((.(((((.--....)))))..))))...((.......))...)).))))))).-.. ( -23.70)
>DroSim_CAF1 13962 97 - 1
AAUGUCCAUGCGAA---AAGCAGGAACAAGAAAG----------UGGC-----AAAUGA--AGAAAGGCCGA--CAACAGGCUGGUUCUGAAGUAUAAUAAACCCCUCUUUUGCCCA-AA
..(((((.(((...---..))))).))).....(----------.(((-----(((.((--((((.((((..--.....))))..))))...((.......))...)).))))))).-.. ( -23.20)
>DroYak_CAF1 15305 105 - 1
AAUGUCCGUGCGAA---AAGCAGGAACAAGAAAG----------UGGCAAGACAAAUGA--AGAAAGGCCAACACAACAGGCUGGUUCUGAAGUAUAAUAAACCCCUCUGUUGGCCAAAA
..(((((.(((...---..))))).)))......----------...............--.....((((((((....(((..((((.............))))))).)))))))).... ( -24.12)
>DroAna_CAF1 14722 113 - 1
AAUGUCCGGCCAGAGCUGGGCGGGGGGAG-GAGGCGGGGCAGGCCGCC-----AGAUGAUGAGAAAGGACGGGGCAACAGGCUGGCACUGAAGUUUCAUAAACUUCUCUUUCCCUCG-CA
.....(((((....)))))((((((((((-(((((((......)))))-----.....((((((.((..(.((.(....).)).)..))....)))))).......)))))))))))-). ( -48.30)
>consensus
AAUGUCCAUGCGAA___AAGCAGGAACAAGAAAG__________UGGC_____AAAUGA__AGAAAGGCCGA__CAACAGGCUGGUUCUGAAGUAUAAUAAACCCCUCUUUUGCCCA_AA
....(((.(((........))))))....................................((((.((((.........))))..))))............................... ( -9.32 = -10.16 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:32 2006